Fig. 2

Comparing results of SEESAW on polyester simulation with different levels of aggregation to mmdiff and WASP. SEESAW was applied at different levels of resolution including transcript (txp), aggregated-to-TSS (TSS), aggregated-to-gene (gene), and “oracle”, where oracle involved aggregating transcripts by the true AI signal direction, known only in simulation. mmdiff was applied at transcript (mmdiff) and gene level (mmdiff_gene), while WASP provided gene level analysis. A iCOBRA plot of sensitivity (true positive rate, or TPR) over achieved false discovery rate (FDR) with three circles indicating 1%, 5%, and 10% nominal FDR cutoffs, respectively. Filled circles indicate observed FDR less than nominal FDR. B Overall sensitivity for all cases of AI and sensitivity stratified by type of AI: “discordant” AI across isoforms within a gene (AI in different directions) or “concordant” AI within gene (AI in the same direction)